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Biomolecules
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The Next Generation of Proteomics for Precision Medicine: Second Edition
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The Next Generation of Proteomics for Precision Medicine: Second Edition

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Biomacromolecules: Proteins, Nucleic Acids and Carbohydrates".

Deadline for manuscript submissions: 30 June 2025 | Viewed by 2918

Special Issue Editor

Dr. Towia Libermann

E-Mail Website
Guest Editor
1. Division of Interdisciplinary Medicine and Biotechnology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
2. Beth Israel Deaconess Medical Center Genomics, Proteomics, Bioinformatics and Systems Biology Center, Boston, MA 02215, USA
3. Harvard Medical School, Boston, MA 02215, USA
Interests: precision medicine; proteomics; biomarkers; diagnostics; systems biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Personalized and precision medicine strive to improve our comprehension and individualized management of disease predisposition, etiology, pathogenesis, onset and progression, treatment response and monitoring, and health outcomes through precise and robust measurements of clinical, personal, molecular, cellular, imaging, environmental, and behavioral factors related to human health and disease. While genomics has been at the forefront of many precision-medicine strategies and discoveries due to the major technological advancements in next-generation sequencing, recent emerging developments in proteomics have begun to have a major impact on precision medicine and are likely to push the limits of proteomics to the next level, ultimately leading to the interrogation of the entire proteome.

Proteins, not DNA or RNA, directly orchestrate the majority of a cell’s functions, and their dysregulations are the ultimate causes of human diseases and the primary targets of most drugs for therapeutic intervention. Protein biomarkers are used in the clinic for many diagnostic applications to diagnose diseases, predict disease development and progression, predict and monitor response to therapy, pair the right patients with the right treatments, and serve as early readouts of drug safety and efficacy.

This Special Issue titled “The Next Generation of Proteomics for Precision Medicine” will highlight and disseminate the latest cutting-edge and innovative developments and findings in this rapidly emerging research field and its applications for human diseases, diagnostics, and drug development. The themes to be covered will include the strengths and limitations of current proteomics technologies; the next generation of innovative proteomics platforms designed for comprehensive and in-depth proteomics; single-molecule protein sequencing; and single-cell proteomics; and the utility and application of proteomics for precision medicine, biomarker discovery, diagnostic development, and drug discovery.

For this thematic collection, we cordially invite researchers to contribute high-quality original research and review articles that cover any relevant topic in state-of-the-art proteomics topics and future perspectives of proteomics.

I look forward to receiving your contributions.

Dr. Towia Libermann
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • proteomics
  • biomarkers
  • next-generation protein sequencing
  • diagnostics
  • protein quantitative trait locus
  • systems biology
  • precision medicine

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Related Special Issue

Published Papers (2 papers)

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Research

26 pages, 6127 KiB  
Article
Exploring the Effects of Metformin on the Body via the Urine Proteome
by Yuzhen Chen, Haitong Wang, Minhui Yang, Ziyun Shen and Youhe Gao
Biomolecules 2025, 15(2), 241; https://doi.org/10.3390/biom15020241 - 7 Feb 2025
Viewed by 759
Abstract
Metformin is the first-line medication for treating type 2 diabetes mellitus, with more than 200 million patients taking it daily. Its effects are extensive and play a positive role in multiple areas. Can its effects and potential mechanisms be explored through the urine [...] Read more.
Metformin is the first-line medication for treating type 2 diabetes mellitus, with more than 200 million patients taking it daily. Its effects are extensive and play a positive role in multiple areas. Can its effects and potential mechanisms be explored through the urine proteome? In this study, 166 differential proteins were identified following the administration of 150 mg/(kg·d) of metformin to rats for five consecutive days. These included complement component C6, pyruvate kinase, coagulation factor X, growth differentiation factor 15, carboxypeptidase A4, chymotrypsin-like elastase family member 1, and L-lactate dehydrogenase C chain. Several of these proteins have been reported to be directly affected by metformin or associated with its effects. Multiple biological pathways enriched by these differential proteins, or proteins containing differentially modified peptides, have been reported to be associated with metformin, such as the glutathione metabolic process, negative regulation of gluconeogenesis, and the renin–angiotensin system. Additionally, some significantly changed proteins and enriched biological pathways, not yet reported to be associated with metformin’s effects, may provide clues for exploring its potential mechanisms. In conclusion, the application of the urine proteome offers a comprehensive and systematic approach to exploring the effects of drugs, providing a new perspective on the study of metformin’s mechanisms. Full article
(This article belongs to the Special Issue The Next Generation of Proteomics for Precision Medicine: Second Edition)
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22 pages, 2920 KiB  
Article
Integrated Multi-Omics Analysis of Cerebrospinal Fluid in Postoperative Delirium
by Bridget A. Tripp, Simon T. Dillon, Min Yuan, John M. Asara, Sarinnapha M. Vasunilashorn, Tamara G. Fong, Sharon K. Inouye, Long H. Ngo, Edward R. Marcantonio, Zhongcong Xie, Towia A. Libermann and Hasan H. Otu
Biomolecules 2024, 14(8), 924; https://doi.org/10.3390/biom14080924 - 30 Jul 2024
Cited by 1 | Viewed by 1783
Abstract
Preoperative risk biomarkers for delirium may aid in identifying high-risk patients and developing intervention therapies, which would minimize the health and economic burden of postoperative delirium. Previous studies have typically used single omics approaches to identify such biomarkers. Preoperative cerebrospinal fluid (CSF) from [...] Read more.
Preoperative risk biomarkers for delirium may aid in identifying high-risk patients and developing intervention therapies, which would minimize the health and economic burden of postoperative delirium. Previous studies have typically used single omics approaches to identify such biomarkers. Preoperative cerebrospinal fluid (CSF) from the Healthier Postoperative Recovery study of adults ≥ 63 years old undergoing elective major orthopedic surgery was used in a matched pair delirium case–no delirium control design. We performed metabolomics and lipidomics, which were combined with our previously reported proteomics results on the same samples. Differential expression, clustering, classification, and systems biology analyses were applied to individual and combined omics datasets. Probabilistic graph models were used to identify an integrated multi-omics interaction network, which included clusters of heterogeneous omics interactions among lipids, metabolites, and proteins. The combined multi-omics signature of 25 molecules attained an AUC of 0.96 [95% CI: 0.85–1.00], showing improvement over individual omics-based classification. We conclude that multi-omics integration of preoperative CSF identifies potential risk markers for delirium and generates new insights into the complex pathways associated with delirium. With future validation, this hypotheses-generating study may serve to build robust biomarkers for delirium and improve our understanding of its pathophysiology. Full article
(This article belongs to the Special Issue The Next Generation of Proteomics for Precision Medicine: Second Edition)
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